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You have a 6 layer design for controlling 24V brushed DC motor, galvanically isolated voltage rails(24V and the rest) and your question is how to separate them properly. 

There is no further reasoning why 6 layer design, why did you choose to isolate the PSU, is there something extremely noise sensitive that you would like to protect in the circuit(right now there is only MCU, RS485 and motor current sense). 

Based on the amount of information given, I don’t think you need 6 layer design, unless you are extremely tight with space or motor draws that much current that you would dedicate the whole plane to it. Even then, you can increase the copper thickness further(4oz is something most manufacturers easily support nowadays). 

Rather use a standard 4 layer design and dedicate one layer to ground, usually the one closest to the layer where components would be mounted.   

I see no valid reason to galvanically isolate the 24V rail, at least you didn’t give one so I would challenge it.  Use a star ground system, where your motor ground and PCB ground would be connected at exactly one place. This would largely prevent motor currents flowing through your circuit. As a bonus, your current sense becomes simpler and cheaper too. 

RS485 could be non isolated as well, but without further information I will let you judge if it makes sense or not.